I have to start small so don't be offended, but did you gap your hto's as needed?
Check all the connectors, I just had a guy stop buy this week for a mis on an 07 and one of the pins in a coil plug was bent causing an intermitant check engine light.. code showed coil failure, only reason I found the bent pin was because it plugged in with more friction to it than the others.
I just did a KB 2.6 on an 06 gt and to date there are no problems with spark blow out. I have a hard time believing your so in the minority with spark blow out without being outside the stock internals thresholds. Usually this surfaces up in the 575 to 600 hp ranges.
If your running the KB canned tune, go get it looked at with your local tuner, I know first hand how bad the canned tune is. It's pretty poor / and way conservative.. Every car is different and your just might not like the canned parameter. Do yourself a favor and at the least flip for a single pull to see where everything is at.
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